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Men in Black II: Alien Escape is partially based on the Men in Black II movie.

In MiB II: Alien Escape players take the role of one of the MiB agents Agent K or Agent J, and are required to stop aliens from blowing up the earth with a ship based weapon called the Class 7 Ozone Demogrifier.

Once the game is started, an intro is played. A large flying saucer loaded with strange types of alien species is hit by an asteroid and is sent flying into the sun. The intro then cuts to MiB headquarters, July, 2002. Zed informs Agents Kay & Jay the incident: The V.S.S Maximus Securitus, the largest prison ship in the galaxy, was hit by an asteroid some Earth years ago and sent into the sun. However, the ship narrowly missed the sun and flew into one of Earth's oceans. When MiB investigated, instead of finding a waterlogged grave, the ship was completely empty. It's up to MiB to round up or destroy any and all aliens that pose a threat to Earth.

Both Kay and Jay use a maximum of 7 weapons combined. The two use other weapons per character. The shared weapons include:

J2 blasters: These are a standard MiB weapon, available in every mission. The projectiles of this weapon are one (for odd-numbered power-ups) and three (even-numbered power-ups). These weapons are seen and used in Men in Black II (elevator scene). This similarity is how Kay has two and Jay has one. Color given is blue.
Xeno bombs: These are powerful weapons and are a one-time only deal. These kill all enemies in the immediate area, without having to spend time and waste health. While this is an extremely powerful weapon, it is also very valuable. If possible, saving these for boss missions would be acceptable. Only three are available per mission. Has no specific color, but has the appearance of a pill.
DRG Fusion Cannon: This is the second given weapon in all the missions. This is not a weapon that can take power-ups, as it is equipped with any weapon of Kay and Jay's. This weapon can target and kill several aliens at once. To use, press and hold down the firing button, release when needed. The charging bar is to the left of the highlighted weapon in use.

Each weapon has six levels, with five power-ups allowed each weapon. The level bar is to the right of the highlighted weapon. These power-ups can be forced out of the character if hit a certain amount of times. Also, many aliens can knock out all power-ups with a single hit for the current weapon with a single hit, minus one. If left out of a character for a certain amount of time, they disappear.